MacOS – “System” storage on macOS Sierra is 470GB!

My setup is the following :

• Macbook pro 2009, 13"
• SSD (Intel X25M Postville) replacing the superdrive, used as system + home folder disk
• Factory HDD used for music and pictures storage

I tried to move my home folder to te HDD, here are my conclusions : when you move your entire home folder to an HDD, your mac boots fast, but you don't get too much performance gain while opening applications (even apps that do not use any document, like safari). That's because when the app starts up, it loads it preference and cache files from your library. If it is on the second drive, startup of apps is nearly as slow as when you use your HDD for booting.

I now use my HDD for iTunes/Aperture and vmware images only. These apps are a bit slower than the others (but still as fast are when I didn't have a SSD). But I did not do as Matt recommends : I created new iTunes and aperture libraries directly on the HDD, using the alt key at launch. I do not like symlinks, that can break if you unmount your HDD, for maintenance or by mistake for example, leaving your home folder in a non consistent state.

Last points :

• with this configuration, you have to be careful of what files you put on the HDD if you have multiple accounts on your mac : these files are accessible to anybody by default, and filevault will not protect them (unless you use Lion which allows full-drive encryption).
• And you need to setup Time machine to include the HDD (if needed), which includes only the system drive by default.

Is there maybe an AppleLocale key in ~/Library/Preferences/ByHost/.GlobalPreferences.*.plist? That would override the key in ~/Library/Preferences/.GlobalPreferences.plist.